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Yorodumi- PDB-3d3d: Bacteriophage lambda lysozyme complexed with a chitohexasaccharide -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d3d | |||||||||
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Title | Bacteriophage lambda lysozyme complexed with a chitohexasaccharide | |||||||||
Components | Lysozyme | |||||||||
Keywords | HYDROLASE / GLYCOSIDASE / TRANSGLYCOSYLASE / LYSOZYME / PROTEIN-CHITOHEXASSACHARIDE COMPLEX / Antimicrobial / Bacteriolytic enzyme | |||||||||
Function / homology | Function and homology information : / lytic transglycosylase activity / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | |||||||||
Biological species | Enterobacteria phage lambda (virus) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | |||||||||
Authors | Leung, A.K.W. / Berghuis, A.M. | |||||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Crystal structure of the lytic transglycosylase from bacteriophage lambda in complex with hexa-N-acetylchitohexaose Authors: Leung, A.K.W. / Duewel, H.S. / Honek, J.F. / Berghuis, A.M. #1: Journal: Biochim.Biophys.Acta / Year: 1995 Title: Investigation of the interactions of saccharides with the lysozyme from bacteriophage lambda Authors: Duewel, H.S. / Daub, E. / Honek, J.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d3d.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d3d.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 3d3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d3d_validation.pdf.gz | 908 KB | Display | wwPDB validaton report |
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Full document | 3d3d_full_validation.pdf.gz | 928.5 KB | Display | |
Data in XML | 3d3d_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 3d3d_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/3d3d ftp://data.pdbj.org/pub/pdb/validation_reports/d3/3d3d | HTTPS FTP |
-Related structure data
Related structure data | 1d9uC 1am7S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17395.701 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage lambda (virus) / Strain: Lambda / Gene: R / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-1 / References: UniProt: P03706, lysozyme #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.16 % |
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 4.6 Details: 0.1 M NaOAc pH 4.6, 0.1 M ammonium sulfate, 20% w/v PEG 2000 MME, microdialysis, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.502 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 30, 1996 / Details: Supper double focusing mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.502 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→33.942 Å / Num. all: 15397 / Num. obs: 11801 / % possible obs: 92 % / Redundancy: 7.7 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.6→2.76 Å / Rmerge(I) obs: 0.507 / Num. unique all: 947 / % possible all: 51.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AM7 Resolution: 2.6→33.94 Å / Rfactor Rfree error: 0.008 / FOM work R set: 0.814 / Data cutoff high absF: 1696147.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 7.732 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→33.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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